Mr Wilkie wrote to the Ombudsman raising concerns that a conflict of interest during a meeting which recommended the the size of the catch was not dealt with properly.

"There can be no doubt that AFMA failed to do its job properly, that the quota for the super trawler is completely discredited and, frankly, that the boat may as well turn around and go back to Europe," he said.

Mr Wilkie also claims that some members of an advisory group to AFMA, the Small Pelagic Fishery Resource Assessment Group, believed the quota was not sustainable.

He says another section of AFMA, the South East Management Advisory Committee, was not told.

"That information was not passed on to the management advisory committee so they didn't have all of the information at their hands when they actually finalised the recommendation for the quota to go to the AFMA commission," he said.

AFMA has welcomed the Ombudsman's decision to investigate its methods for setting quotas.

In a statement, AFMA says it is confident the catch limits were set lawfully and it welcomes the Ombudsman's scrutiny.

It says the quotas were determined using all of the available scientific information and is adamant that there was no conflict of interest.

Senator Colbeck is the Opposition's fisheries secretary and has told ABC Local Radio he doubts there is cause for concern.

"I've read through those minutes and I've seen that all the declarations of interest were declared," he said.

"So I'm not sure that I would agree with Mr Wilkie in respect of the concerns that he's expressing, but I'm very happy for the process that's occurring now to be dealt with properly."

Tasmanian Labor Senator Lin Thorp maintains Labor is doing everything in its power to address concerns.

Senator Thorp says she and party colleagues have approached the Prime Minister and the Fisheries and Environment Ministers with concerns about localised overfishing and the possibility that the science used to determine the quota is old.

Meanwhile, there will be an attempt in the Senate to block the super trawler's quotas.

Destructive or sustainable?

The size of the Margiris, now named Abel Tasman, has sparked fears it will decimate fish stocks.

But Australia's fishing regulator says the trawler's quota is based on sound science.

So will the super trawler devastate a region, or will its catch be a drop in the ocean?

The Australian Greens are set tomorrow to move a disallowance motion which would stop the quotas for the Small Pelagic Fishery, such as jack mackerel and redbait, passing into law.

If it passes, a new set of quotas will not be able to be set within six months, unless approved by federal parliament, throwing into doubt the ability of Seafish Tasmania and other licence holders to operate.

Greens Senator Peter Whish-Wilson says he is concerned the science behind the quota system has not taken into account concerns about local fish stock depletion.

"What we're trying to do now is come up with a list of concerns and try to find out if we have common ground with other parties in the Senate and, if we do and we get support for our disallowance motion, then that puts a lot of pressure back on the Government."

AFMA says it has used the best available science to set the catch limits.

Tasmania's main business lobby is urging the community to ignore the hype surrounding the super trawler heading to Devonport.

Seafish Tasmania is a member of the Chamber of Commerce and Industry.

TCCI spokesman Neil MacKinnon has told ABC Local Radio Seafish should be allowed to trawl while the Ombudsman's investigation is underway.

"If the Ombudsman says that process has been deficient in some way, we would say that the quota should be modified," he said.

"But it's so important for Tasmania generally that we get away from this precautionary principle that says 'let's not do anything in case', rather than adopting a principle that says 'let's do it, but make sure we do it well'."